I don't believe that there are income limits for FHA financing and you can actually put down as little as 3.5% OR as much as you want. There are loan limits. In San Francisco, it's $729,750 for a single family home or condo.
Where did you get this information? It sounds like you need the assistance of an experienced mortgage broker. If you need recommendations, check out my site or contact me offline.
PS. I help many first time buyers who use FHA loans (especially great products for single family homes). You need a great team (Realtor and Mortgage Broker) to make the process successful and enjoyable here in San Francisco. Look me up if you're not already happily working with someone. And if you are, they should be able to answer these questions for you! :)
Danielle Lazier, San Francisco Realtor
Zephyr Real Estate
415.731.5000 x158 danielle(at)zephyrsf.com